I agree with edrandall, however I gave it more then a 60 second test. I had two non-system 750GB drives with similar contents (both around 400GB used of various contents: ISO, videos, zips, etc). I ran the CRC compare of the two drives and left it overnight. Next morning when I came to work I found my C:\ drive (system) filled up with BC3* tmp files totaling 150GB and system almost unusable, not to mention Beyond Compare did finish with bunch of "stream read/write errors".
After above happened, I looked in the application options to change temporary folder location or any settings but those simply did not exist.
I'm continuing to search for other folder comparison tools with small footprint similarly good UI and ability to tweak temp folder use so that it doesn't negatively impact system performance.